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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Publications at this Location » Publication #274337
Title: SNP discovery in avocado from second generation sequencing of the leaf and flower transcriptome

Author
item Kuhn, David
item Livingstone, Donald
item MOCKAITIS, KEITHANNE - Indiana University
item Tondo, Cecile
item Schnell Ii, Raymond

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/16/2011
Publication Date: 1/16/2011
Citation: Kuhn, D.N., Livingstone, D., Mockaitis, K., Tondo, C.L., Schnell II, R.J. 2011. SNP discovery in avocado from second generation sequencing of the leaf and flower transcriptome. Annual International Plant & Animal Genome Conference. 2011.

Interpretive Summary: We have generated two large mapping populations for avocado: a California mapping population of reciprocal crosses of Hass and Bacon (~1000 individuals) and a Florida mapping population of reciprocal crosses of Simmonds and Tonnage (~1000 individuals). These mapping populations will allow us to associate particular genetic markers with phenotypic traits such as cold tolerance, high oil content, fatty acid composition and flowering type. Development of such markers will provide breeders with a way to screen new seedlings for favorable alleles in an avocado breeding program. This will accelerate progress in breeding of new avocado varieties with improved disease resistance and nutritional qualities.

Technical Abstract: We have generated two large mapping populations for avocado: a California mapping population of reciprocal crosses of Hass and Bacon (~1000 individuals) and a Florida mapping population of reciprocal crosses of Simmonds and Tonnage (~1000 individuals). Initial genotyping was done using microsatellite markers but there are only about 150 markers currently available. Single nucleotide polymorphism (SNP) markers occur more frequently than microsatellite markers and can be assayed using high throughput platforms. We previously identified ~50,000 high quality SNP markers as part of the cacao genome sequencing project by second generation sequencing of the cacao leaf transcriptome. The SNPs were used to design a 6K SNP chip for genotyping our cacao mapping populations. We have used a similar approach for avocado. RNA was isolated from leaves, unopened flowers, female flowers and male flowers of Hass, Bacon, Simmonds and Tonnage at SHRS and sent to Indiana University for library preparation and sequencing. The Hass RNA was sequenced on a 454 Titanium platform and assembled using Newbler to provide a reference transcriptome. All other RNAs were sequenced on an Illumina GAII platform and reads aligned to the Hass transcriptome for SNP identification.